Analyzing the molecular mechanism of the tissue specificity of gastrointestinal stromal tumors by using bioinformatics approaches.

Purpose: Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. About 70% of GIST occur in the stomach, 20% in the small intestine and less than 10% in the esophagus. This study aimed to explore the difference of gene expression profile of GIST between different tumor sites. Methods: Microarray data GSE8167 (accession number of the microarray data) were available from Gene Expression Omnibus (GEO) which included 23 gastric and 9 small intestine untreated GIST samples, and then the differentially expressed genes (DEGs) between these samples were identified using t-test. Furthermore, pathway enrichment analysis was performed to these DEGs and one protein-protein interaction network was constructed by STRING. Additionally, BioNet in R was used to establish a sub-network with false discovery rate < 0.001, and genes in this sub-network were further subjected to gene ontology (GO) and pathway analyses. Results: A total 730 genes were differentially expressed be-tween gastric samples and small intestine samples, indicating the tissue specifity of GIST. Pathway analysis suggested these DEGs disturbed ECM-receptor interaction, gap junction and colorectal cancer. Moreover, some nodes (such as PLAT, VEGFC, PGF and CHD7) in the sub-network were significantly enriched in blood vessel development (p=4.58E-06), appendage development (p=9.54E-06) and skeletal system development (p=2.40E-04), respectively. Finally, several DEGs in the sub-network, including VEGFC and PGF, mainly affected pathways in cancer, focal adhesion, bladder cancer and cytokine-cytokine receptor interaction. Conclusions: Our results suggest that molecular mechanisms of GIST originating in different site were different. Our findings are helpful for physicians and researchers to study the tissue specificity of GIST.